snATACseq QC with ArchR. Altering LSI parameter: Iteration

Results

QC

ArchR pre-filters the cells using thresholds:

  • TSS Enrichment > 4
  • Min frags per cell > 1000

Counts

Sample Cells_Pass_Filter Cells_dropped Total_Frags Median_Frags Median_TSS_Enrichment
510_FC 7011 219 141701588 15242 14.259
611_FC 3869 161 89911016 16830 11.868
993_FC 5273 207 62967252 5871 9.037

PARAMETER

Iteration : 2
## Warning in kable_pipe(x = structure(c("RNA", "ATAC", "N-undef", "C1", "ExN-1", :
## The table should have a header (column names)

RNA N-undef ExN-1 RG-1 ExN-2 InN-3 InN-3 ExN-4 ExN-5 ExN-2 RG-2 RG-1 RG-1 MG InN-1 InN-2 InN-2
ATAC C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16
Iteration : 4
## Warning in kable_pipe(x = structure(c("RNA", "ATAC", "MG", "C1", "RG-1", : The
## table should have a header (column names)

RNA MG RG-1 RG-2 InN-1 InN-2 InN-2 ExN-4 ExN-5 InN-3 ExN-2 InN-3 InN-3 ExN-5 N-undef ExN-4 RG-1 ExN-1
ATAC C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 C17
Iteration : 6
## Warning in kable_pipe(x = structure(c("RNA", "ATAC", "RG-2", "C1", "RG-1", : The
## table should have a header (column names)

RNA RG-2 RG-1 RG-1 MG ExN-4 ExN-5 ExN-3 ExN-5 ExN-2 ExN-2 InN-3 InN-1 InN-2 InN-2 ExN-1 RG-1 ExN-1
ATAC C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 C17
Iteration : 8
## Warning in kable_pipe(x = structure(c("RNA", "ATAC", "InN-3", "C1", "ExN-2", :
## The table should have a header (column names)

RNA InN-3 ExN-2 ExN-4 ExN-5 N-undef ExN-2 InN-2 ExN-1 ExN-2 InN-3 MG InN-1 InN-2 InN-2 RG-2 RG-1 RG-1
ATAC C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 C17
Iteration : 10
## Warning in kable_pipe(x = structure(c("RNA", "ATAC", "InN-3", "C1", "ExN-1", :
## The table should have a header (column names)

RNA InN-3 ExN-1 RG-1 ExN-3 ExN-2 InN-3 InN-3 ExN-4 ExN-5 ExN-2 RG-2 RG-1 RG-1 MG InN-1 InN-2 InN-2
ATAC C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 C17